Half-Life 2: Episode One
I can clearly see that Valve improved upon HL2 in episodes one and two. There is a clear evolution in their storytelling techniques. Level design, scripted events, dialogues, characters. Everything evolved. However, this isn't a flawless game.
I really liked the synergy with Alyx. Playing episode one alongside Alyx and the robot felt similar to other games where the main character is not alone throughout the game. I liked the puzzles and how the gravity gun is used to solve them. There is one caveat though. This idea of using the gravity gun to grab the plasma balls and using the plasma ball to power up some device. I played Portal before episode one. Have I not played Portal before, I'd probably have had a harder time solving the puzzles in episode one. I think that they overlooked this detail.
The environment art department is excellent. The inside of the cidatel's architecture is superb. It's clean and doesn't have excessive details that would distract the players from the main path. Somehow I see similarities between The Cidatel and Halo's ancient structures. The sky in episode one has had the same breathtaking impact on me that the sky of HL2 had.
There is one thing that I dislike though. I'm not a fan of how Valve wants to tell a story without shifting to cutscenes. To give an example: you reach a location and there is a scripted event to have the NPCs talking. Valve doesn't want to shift the camera to another angle to do a cutscene. The player is free to walk around. The thing is, there is nothing of importance to do or see while the NPCs are talking!
In addition, I'm not a fan of never giving Gordon Freeman lines and a personality. Half-life have its origins tied to the developers liking doom and in doom the character does not have a voice or a personality. I really wanted to see Gordon Freeman as a fully developed character and not just a player's avatar.
The last part was confusing for me. The waves of enemies coming from the building is endless. I wasted time there. When I realized the enemies would keep coming forever I just ignored them and proceeded to rescue the NPCs. The final boss is a Strider and it was also confusing. I wasted time and effort trying to defeat the Strider while avoid its attacks. When I finally reached the final ladder, after dying multiple times, there was a crate with infinite ammo. Looking back, I can see that the level design aspect of Half Life 2 still has some rough edges here and there.
If you want to learn more about game design, check the developer commentary of HL2, episode one and episode two. Those are goldmines. Take the time to listen to them and see how they created the game.